Starting phenix.real_space_refine (version: dev) on Wed Feb 22 02:35:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2023/7byn_30246_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2023/7byn_30246.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2023/7byn_30246_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2023/7byn_30246_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2023/7byn_30246_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2023/7byn_30246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2023/7byn_30246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2023/7byn_30246_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2023/7byn_30246_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E GLU 551": "OE1" <-> "OE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G ARG 168": "NH1" <-> "NH2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G GLU 328": "OE1" <-> "OE2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G GLU 551": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16349 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "C" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "E" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "G" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "B" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "D" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "F" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "H" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' K': 3, 'PT5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'FCC': 1, 'PT5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 9.27, per 1000 atoms: 0.57 Number of scatterers: 16349 At special positions: 0 Unit cell: (135.875, 135.875, 125.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 92 16.00 P 12 15.00 O 2985 8.00 N 2747 7.00 C 10510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 2.3 seconds 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 4 sheets defined 74.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 96 through 120 removed outlier: 3.708A pdb=" N PHE A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 114 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 155 removed outlier: 3.837A pdb=" N ILE A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 173 through 192 Processing helix chain 'A' and resid 200 through 217 removed outlier: 4.134A pdb=" N ARG A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N PHE A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN A 210 " --> pdb=" O MET A 206 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 214 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 260 removed outlier: 3.568A pdb=" N HIS A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 310 through 335 Proline residue: A 314 - end of helix removed outlier: 3.527A pdb=" N LEU A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 333 " --> pdb=" O HIS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 removed outlier: 3.612A pdb=" N ILE A 346 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 351 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 354 " --> pdb=" O ARG A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 528 through 553 removed outlier: 4.182A pdb=" N LEU A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 586 Processing helix chain 'C' and resid 75 through 92 Processing helix chain 'C' and resid 96 through 120 removed outlier: 3.573A pdb=" N PHE C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 155 removed outlier: 3.837A pdb=" N ILE C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY C 155 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 170 Processing helix chain 'C' and resid 173 through 192 Processing helix chain 'C' and resid 200 through 217 removed outlier: 4.134A pdb=" N ARG C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE C 208 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN C 210 " --> pdb=" O MET C 206 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE C 211 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET C 214 " --> pdb=" O GLN C 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 260 removed outlier: 3.568A pdb=" N HIS C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 294 through 307 Processing helix chain 'C' and resid 310 through 335 Proline residue: C 314 - end of helix removed outlier: 3.528A pdb=" N LEU C 318 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS C 333 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 356 removed outlier: 3.611A pdb=" N ILE C 346 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 351 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 354 " --> pdb=" O ARG C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 528 through 553 removed outlier: 4.293A pdb=" N LEU C 553 " --> pdb=" O PHE C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 586 Processing helix chain 'E' and resid 75 through 91 Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.668A pdb=" N SER E 111 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 155 removed outlier: 3.837A pdb=" N ILE E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY E 155 " --> pdb=" O VAL E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 170 Processing helix chain 'E' and resid 173 through 192 Processing helix chain 'E' and resid 200 through 217 removed outlier: 4.134A pdb=" N ARG E 207 " --> pdb=" O LEU E 203 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE E 208 " --> pdb=" O ARG E 204 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU E 209 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE E 211 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 260 removed outlier: 3.568A pdb=" N HIS E 234 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS E 236 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 294 through 307 Processing helix chain 'E' and resid 310 through 335 Proline residue: E 314 - end of helix removed outlier: 3.526A pdb=" N LEU E 318 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS E 333 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 356 removed outlier: 3.611A pdb=" N ILE E 346 " --> pdb=" O ALA E 343 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 351 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 354 " --> pdb=" O ARG E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 361 No H-bonds generated for 'chain 'E' and resid 359 through 361' Processing helix chain 'E' and resid 528 through 553 removed outlier: 4.176A pdb=" N LEU E 553 " --> pdb=" O PHE E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 586 Processing helix chain 'G' and resid 75 through 92 Processing helix chain 'G' and resid 96 through 120 Processing helix chain 'G' and resid 125 through 155 removed outlier: 3.837A pdb=" N ILE G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY G 155 " --> pdb=" O VAL G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 170 Processing helix chain 'G' and resid 173 through 192 Processing helix chain 'G' and resid 200 through 217 removed outlier: 4.134A pdb=" N ARG G 207 " --> pdb=" O LEU G 203 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N PHE G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU G 209 " --> pdb=" O SER G 205 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN G 210 " --> pdb=" O MET G 206 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU G 212 " --> pdb=" O PHE G 208 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET G 214 " --> pdb=" O GLN G 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET G 217 " --> pdb=" O ARG G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 260 removed outlier: 3.568A pdb=" N HIS G 234 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS G 236 " --> pdb=" O TYR G 232 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU G 237 " --> pdb=" O ALA G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 281 Processing helix chain 'G' and resid 294 through 307 Processing helix chain 'G' and resid 310 through 335 Proline residue: G 314 - end of helix removed outlier: 3.528A pdb=" N LEU G 318 " --> pdb=" O ALA G 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS G 333 " --> pdb=" O HIS G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 356 removed outlier: 3.611A pdb=" N ILE G 346 " --> pdb=" O ALA G 343 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG G 351 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER G 354 " --> pdb=" O ARG G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 528 through 553 removed outlier: 4.200A pdb=" N LEU G 553 " --> pdb=" O PHE G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 586 Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.605A pdb=" N PHE B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 38 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'D' and resid 6 through 19 removed outlier: 3.603A pdb=" N PHE D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 79 through 92 removed outlier: 4.071A pdb=" N PHE D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'F' and resid 6 through 19 removed outlier: 3.604A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 45 through 54 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'F' and resid 118 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'H' and resid 6 through 19 removed outlier: 3.605A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 38 Processing helix chain 'H' and resid 45 through 54 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 79 through 92 removed outlier: 4.071A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'H' and resid 118 through 127 Processing helix chain 'H' and resid 138 through 145 Processing sheet with id= A, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= B, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= C, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= D, first strand: chain 'H' and resid 99 through 101 1055 hydrogen bonds defined for protein. 2553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2629 1.31 - 1.44: 4639 1.44 - 1.57: 9240 1.57 - 1.70: 18 1.70 - 1.83: 160 Bond restraints: 16686 Sorted by residual: bond pdb=" C15 FCC C 702 " pdb=" N02 FCC C 702 " ideal model delta sigma weight residual 1.415 1.512 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C22 PT5 G 701 " pdb=" C23 PT5 G 701 " ideal model delta sigma weight residual 1.592 1.497 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C22 PT5 C 701 " pdb=" C23 PT5 C 701 " ideal model delta sigma weight residual 1.592 1.497 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C22 PT5 E 701 " pdb=" C23 PT5 E 701 " ideal model delta sigma weight residual 1.592 1.498 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C22 PT5 A 701 " pdb=" C23 PT5 A 701 " ideal model delta sigma weight residual 1.592 1.498 0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 16681 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.48: 297 106.48 - 113.41: 9239 113.41 - 120.34: 6818 120.34 - 127.28: 6008 127.28 - 134.21: 162 Bond angle restraints: 22524 Sorted by residual: angle pdb=" C18 PT5 E 701 " pdb=" C19 PT5 E 701 " pdb=" C20 PT5 E 701 " ideal model delta sigma weight residual 85.86 125.61 -39.75 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C18 PT5 C 701 " pdb=" C19 PT5 C 701 " pdb=" C20 PT5 C 701 " ideal model delta sigma weight residual 85.86 125.60 -39.74 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C18 PT5 G 701 " pdb=" C19 PT5 G 701 " pdb=" C20 PT5 G 701 " ideal model delta sigma weight residual 85.86 125.60 -39.74 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C18 PT5 A 701 " pdb=" C19 PT5 A 701 " pdb=" C20 PT5 A 701 " ideal model delta sigma weight residual 85.86 125.59 -39.73 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C15 PT5 E 701 " pdb=" C16 PT5 E 701 " pdb=" C17 PT5 E 701 " ideal model delta sigma weight residual 152.67 125.53 27.14 3.00e+00 1.11e-01 8.18e+01 ... (remaining 22519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 9209 35.77 - 71.53: 559 71.53 - 107.30: 28 107.30 - 143.06: 6 143.06 - 178.83: 8 Dihedral angle restraints: 9810 sinusoidal: 4022 harmonic: 5788 Sorted by residual: dihedral pdb=" C13 PT5 A 701 " pdb=" C14 PT5 A 701 " pdb=" C15 PT5 A 701 " pdb=" C16 PT5 A 701 " ideal model delta sinusoidal sigma weight residual 161.05 -20.12 -178.83 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C18 PT5 E 701 " pdb=" C19 PT5 E 701 " pdb=" C20 PT5 E 701 " pdb=" C21 PT5 E 701 " ideal model delta sinusoidal sigma weight residual -7.32 169.39 -176.71 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C13 PT5 E 701 " pdb=" C14 PT5 E 701 " pdb=" C15 PT5 E 701 " pdb=" C16 PT5 E 701 " ideal model delta sinusoidal sigma weight residual 161.05 -25.40 -173.55 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1710 0.044 - 0.089: 564 0.089 - 0.133: 130 0.133 - 0.177: 61 0.177 - 0.222: 23 Chirality restraints: 2488 Sorted by residual: chirality pdb=" CA VAL G 583 " pdb=" N VAL G 583 " pdb=" C VAL G 583 " pdb=" CB VAL G 583 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL A 583 " pdb=" N VAL A 583 " pdb=" C VAL A 583 " pdb=" CB VAL A 583 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL E 583 " pdb=" N VAL E 583 " pdb=" C VAL E 583 " pdb=" CB VAL E 583 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2485 not shown) Planarity restraints: 2824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 PT5 G 701 " 0.100 2.00e-02 2.50e+03 2.35e-01 5.50e+02 pdb=" C15 PT5 G 701 " -0.314 2.00e-02 2.50e+03 pdb=" C16 PT5 G 701 " 0.318 2.00e-02 2.50e+03 pdb=" C17 PT5 G 701 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 PT5 A 701 " 0.100 2.00e-02 2.50e+03 2.33e-01 5.42e+02 pdb=" C15 PT5 A 701 " -0.312 2.00e-02 2.50e+03 pdb=" C16 PT5 A 701 " 0.314 2.00e-02 2.50e+03 pdb=" C17 PT5 A 701 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 PT5 E 701 " 0.213 2.00e-02 2.50e+03 2.13e-01 4.53e+02 pdb=" C21 PT5 E 701 " -0.212 2.00e-02 2.50e+03 pdb=" C22 PT5 E 701 " -0.213 2.00e-02 2.50e+03 pdb=" C23 PT5 E 701 " 0.213 2.00e-02 2.50e+03 ... (remaining 2821 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.59: 196 2.59 - 3.23: 16971 3.23 - 3.86: 31821 3.86 - 4.50: 41611 4.50 - 5.14: 64534 Nonbonded interactions: 155133 Sorted by model distance: nonbonded pdb=" O THR G 282 " pdb=" OG1 THR G 283 " model vdw 1.949 2.440 nonbonded pdb=" O THR E 282 " pdb=" OG1 THR E 283 " model vdw 1.949 2.440 nonbonded pdb=" O THR C 282 " pdb=" OG1 THR C 283 " model vdw 1.950 2.440 nonbonded pdb=" O THR A 282 " pdb=" OG1 THR A 283 " model vdw 1.950 2.440 nonbonded pdb=" CE LYS C 78 " pdb=" OD1 ASP D 131 " model vdw 2.024 3.440 ... (remaining 155128 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 588 or resid 701)) selection = (chain 'C' and (resid 74 through 588 or resid 701)) selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 12 5.49 5 S 92 5.16 5 C 10510 2.51 5 N 2747 2.21 5 O 2985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.220 Check model and map are aligned: 0.240 Process input model: 41.840 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5171 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.097 16686 Z= 0.730 Angle : 1.289 39.753 22524 Z= 0.688 Chirality : 0.053 0.222 2488 Planarity : 0.011 0.235 2824 Dihedral : 20.658 178.829 6074 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.90 % Favored : 96.90 % Rotamer Outliers : 16.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 1968 helix: -0.43 (0.11), residues: 1500 sheet: None (None), residues: 0 loop : 0.42 (0.30), residues: 468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 268 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 278 outliers final: 111 residues processed: 478 average time/residue: 0.3213 time to fit residues: 219.0318 Evaluate side-chains 292 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 181 time to evaluate : 1.706 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 0 residues processed: 111 average time/residue: 0.1600 time to fit residues: 34.4405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 114 optimal weight: 0.7980 chunk 177 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 292 HIS A 329 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS C 125 GLN C 234 HIS C 329 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN E 102 HIS E 125 GLN E 329 GLN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 HIS ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5200 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16686 Z= 0.203 Angle : 0.628 14.119 22524 Z= 0.318 Chirality : 0.037 0.154 2488 Planarity : 0.005 0.052 2824 Dihedral : 12.537 134.283 2306 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 0.81 % Favored : 98.98 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.19), residues: 1968 helix: 1.13 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : 1.36 (0.31), residues: 496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 217 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 16 residues processed: 252 average time/residue: 0.2804 time to fit residues: 105.3892 Evaluate side-chains 195 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.776 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1772 time to fit residues: 7.3986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 192 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN G 234 HIS D 137 ASN H 107 HIS H 143 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5247 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 16686 Z= 0.197 Angle : 0.573 12.832 22524 Z= 0.288 Chirality : 0.035 0.137 2488 Planarity : 0.004 0.034 2824 Dihedral : 10.689 127.308 2306 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.17 % Favored : 98.63 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.19), residues: 1968 helix: 1.40 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : 1.40 (0.31), residues: 476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 185 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 24 residues processed: 217 average time/residue: 0.2475 time to fit residues: 83.9683 Evaluate side-chains 195 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1439 time to fit residues: 9.1366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 169 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 16686 Z= 0.179 Angle : 0.555 12.534 22524 Z= 0.278 Chirality : 0.034 0.137 2488 Planarity : 0.004 0.029 2824 Dihedral : 9.435 126.939 2306 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 0.86 % Favored : 98.93 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.19), residues: 1968 helix: 1.43 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : 1.40 (0.31), residues: 476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 200 average time/residue: 0.2712 time to fit residues: 86.0839 Evaluate side-chains 174 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 1.681 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1473 time to fit residues: 4.1000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 130 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN F 143 GLN H 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5286 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16686 Z= 0.202 Angle : 0.558 12.570 22524 Z= 0.281 Chirality : 0.034 0.138 2488 Planarity : 0.004 0.033 2824 Dihedral : 8.743 126.211 2306 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.12 % Favored : 98.68 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.19), residues: 1968 helix: 1.43 (0.14), residues: 1500 sheet: None (None), residues: 0 loop : 1.41 (0.31), residues: 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 203 average time/residue: 0.2469 time to fit residues: 78.5449 Evaluate side-chains 183 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1463 time to fit residues: 6.1284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.0870 chunk 170 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5321 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 16686 Z= 0.216 Angle : 0.581 12.371 22524 Z= 0.291 Chirality : 0.035 0.141 2488 Planarity : 0.004 0.037 2824 Dihedral : 8.498 126.340 2306 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.27 % Favored : 98.53 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.19), residues: 1968 helix: 1.39 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : 1.27 (0.30), residues: 472 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 190 average time/residue: 0.2481 time to fit residues: 74.4961 Evaluate side-chains 173 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1478 time to fit residues: 4.6116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 188 optimal weight: 0.7980 chunk 118 optimal weight: 0.0010 chunk 115 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5285 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 16686 Z= 0.161 Angle : 0.549 12.511 22524 Z= 0.275 Chirality : 0.033 0.133 2488 Planarity : 0.004 0.038 2824 Dihedral : 8.217 128.169 2306 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.17 % Favored : 98.63 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 1968 helix: 1.55 (0.14), residues: 1496 sheet: None (None), residues: 0 loop : 1.20 (0.29), residues: 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 1.866 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 193 average time/residue: 0.2676 time to fit residues: 82.6891 Evaluate side-chains 173 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 2.110 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1719 time to fit residues: 5.0937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5299 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16686 Z= 0.173 Angle : 0.566 12.452 22524 Z= 0.281 Chirality : 0.034 0.140 2488 Planarity : 0.004 0.041 2824 Dihedral : 8.115 126.748 2306 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.27 % Favored : 98.58 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.19), residues: 1968 helix: 1.52 (0.14), residues: 1496 sheet: None (None), residues: 0 loop : 1.20 (0.29), residues: 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 1.817 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 178 average time/residue: 0.2448 time to fit residues: 69.6589 Evaluate side-chains 171 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1389 time to fit residues: 3.5735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.0030 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 ASN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5315 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 16686 Z= 0.188 Angle : 0.580 12.421 22524 Z= 0.286 Chirality : 0.034 0.189 2488 Planarity : 0.004 0.042 2824 Dihedral : 8.068 125.911 2306 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.47 % Favored : 98.42 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 1968 helix: 1.55 (0.14), residues: 1496 sheet: None (None), residues: 0 loop : 1.21 (0.30), residues: 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 173 time to evaluate : 1.770 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 177 average time/residue: 0.2363 time to fit residues: 66.7597 Evaluate side-chains 169 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1494 time to fit residues: 3.2667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 195 optimal weight: 0.0980 chunk 179 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 ASN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN H 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5307 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 16686 Z= 0.176 Angle : 0.588 12.422 22524 Z= 0.288 Chirality : 0.034 0.211 2488 Planarity : 0.004 0.042 2824 Dihedral : 7.960 126.182 2306 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.32 % Favored : 98.63 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.19), residues: 1968 helix: 1.54 (0.14), residues: 1496 sheet: None (None), residues: 0 loop : 1.16 (0.29), residues: 472 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 166 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 170 average time/residue: 0.2575 time to fit residues: 69.6672 Evaluate side-chains 166 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.950 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1447 time to fit residues: 2.9584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 143 optimal weight: 0.0020 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 ASN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.214041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124131 restraints weight = 26332.932| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.44 r_work: 0.3313 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4616 r_free = 0.4616 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4614 r_free = 0.4614 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.4614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 16686 Z= 0.164 Angle : 0.575 12.443 22524 Z= 0.282 Chirality : 0.034 0.197 2488 Planarity : 0.004 0.045 2824 Dihedral : 7.775 125.917 2306 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.47 % Favored : 98.48 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.19), residues: 1968 helix: 1.53 (0.14), residues: 1504 sheet: None (None), residues: 0 loop : 1.17 (0.30), residues: 464 =============================================================================== Job complete usr+sys time: 3441.73 seconds wall clock time: 62 minutes 46.65 seconds (3766.65 seconds total)